I have an illumina genotype final report, and I want to convert it to .ped using plink.
I prepared three files; fam, lgen, and fam (please find below a snap shot for these files )
Then I used plink, but O got the error Variant 'rs1000002' in .lgen file has 3+ different alleles.
Although, as you can see from the first line of lgen file, Variant 'rs1000002' has only two alleles

(As for why plink 2.0 doesn't have the --file flag yet, that's lower priority because plink 1.9 already has a good implementation. The first development priority is enabling important things that can't be done at all with plink 1.9.)

Hi Christopher,
How can I create a lgen file which has only one individual genotyped for 300,000 SNPs.
I mean in the context of sample ids, what shall I use?
I created the lgen, fam files below. Then I used plink 1.9 to generate ped file (log file shown belos). The problem is that genotypes in ped file mismatch genotype in lgen file.

lgen_file:
200638550003_R01C01 200638550003_R01C01 rs1000002 A G

200638550003_R01C01 200638550003_R01C01 rs1000003 A G

200638550003_R01C01 200638550003_R01C01 rs10000030 A G

200638550003_R01C01 200638550003_R01C01 rs10000037 G G

fam_file:
200638550003_R01C01 200638550003_R01C01 0 0 0 0

map_file

3 rs1000002 0 183635768

3 rs1000003 0 98342907

4 rs10000030 0 103374154

4 rs10000037 0 38924330

ped_file:
200638550003_R01C01 200638550003_R01C01 0 0 0 -9 A A G A G A G A G G G A G A A A A A G G